test_new.py 文件源码

def testNewDNA(self):

        self.setUpPhylotyper(aa=False)

        # Set up subtype files
        build_pipeline(self.subtype_options, self.configObj)

        # Save setup
        self.subtypeOptionsObj.save()

        # Check output files
        filepaths = self.subtypeOptionsObj.get_subtype_config(self.scheme)
        fasta = SeqIO.index(filepaths['alignment'][0], 'fasta')

        with open(filepaths['subtype']) as f:
            for i, l in enumerate(f):
                pass

        sd = SeqDict()
        sd.load(filepaths['lookup'])

        n = 120
        self.assertTrue(all([len(fasta) == n, i+1 == n, len(sd.seqs) == n]))